Interferon-induced guanylate-binding proteins in inflammasome activation and host defense.

Traditional views of the inflammasome highlight the assembly of pre-existing core components shortly after infection or tissue damage. Emerging work, however, suggests that the inflammasome machinery is also subject to 'tunable' or inducible signals that might accelerate its autocatalytic properties and dictate where inflammasome assembly takes place in the cell. Many of these signals operate downstream of interferon receptors to elicit inflammasome regulators, including a new family of interferon-induced GTPases called 'guanylate-binding proteins' (GBPs). Here we investigate the critical roles of interferon-induced GBPs in directing inflammasome subtype-specific responses and their consequences for cell-autonomous immunity to a wide variety of microbial pathogens. We discuss emerging mechanisms of action and the potential effect of these GBPs on predisposition to sepsis and other infectious or inflammatory diseases.

Overexpression of PeRHD3 alters the root architecture in Populus.

Adventitious rooting is essential for the vegetative propagation of economically important woody species. A better understanding of the genetic and physiological mechanisms that promote or hinder rooting will enhance the potential for successful commercial deployment of trees. ROOT HAIR DEFECTIVE 3 (RHD3), a large GTP-binding protein, is ubiquitously expressed in plants. Our previous microarray study identified differential expression patterns of genes belonging to the RHD3 family during adventitious root development from hardwood cuttings, and indicated that the RHD3 genes were involved in adventitious rooting in Populus. In this study, we cloned and characterized cDNAs of the two Populus RHD3 genes, designated as PeRHD3a and PeRHD3b. Transcripts encoded by the two genes were detected in roots, stems, leaves and petioles. To characterize the cellular functions of the genes, Agrobacterium tumifaciens was used to transform poplar with a vector that places expression of the target gene under the control of the strong constitutive promoter, Cauliflower Mosaic Virus 35S (Pro35S) promoter. Both PeRHD3a transgenic lines and PeRHD3b transgenic lines showed very similar phenotypic characteristics. Overexpression of PeRHD3a or PeRHD3b in poplar plants resulted in the formation of only a single prominent adventitious root with well-developed lateral roots, characteristic abnormalities in the root tip, and longer and more plentiful root hairs. These results imply that RHD3 may control adventitious and lateral root formation, as well as root hair development by regulating anisotropic cell expansion.

Classification of G proteins and prediction of GPCRs-G proteins coupling specificity using continuous wavelet transform and information theory.

The coupling between G protein-coupled receptors (GPCRs) and guanine nucleotide-binding proteins (G proteins) regulates various signal transductions from extracellular space into the cell. However, the coupling mechanism between GPCRs and G proteins is still unknown, and experimental determination of their coupling specificity and function is both expensive and time consuming. Therefore, it is significant to develop a theoretical method to predict the coupling specificity between GPCRs and G proteins as well as their function using their primary sequences. In this study, a novel four-layer predictor (GPCRsG_CWTIT) based on support vector machine (SVM), continuous wavelet transform (CWT) and information theory (IT) is developed to classify G proteins and predict the coupling specificity between GPCRs and G proteins. SVM is used for construction of models. CWT and IT are used to characterize the primary structure of protein. Performance of GPCRsG_CWTIT is evaluated with cross-validation test on various working dataset. The overall accuracy of the G proteins at the levels of class and family is 98.23 and 85.42%, respectively. The accuracy of the coupling specificity prediction varies from 74.60 to 94.30%. These results indicate that the proposed predictor is an effective and feasible tool to predict the coupling specificity between GPCRs and G proteins as well as their functions using only the protein full sequence. The establishment of such an accurate prediction method will facilitate drug discovery by improving the ability to identify and predict protein-protein interactions. GPCRsG_CWTIT and dataset can be acquired freely on request from the authors.

The fifth class of Galpha proteins.

All alpha-subunits of vertebrate heterotrimeric G proteins have been classified into 4 major classes, Gs, Gi, Gq, and G12, which possess orthologs already in sponges, one of the earliest animal phyla to evolve. Here we report the discovery of the fifth class of Galpha protein, Gv, ancient like the other 4 classes, with members already in sponges, and encoded by 1-2 gnav genes per species. Gv is conserved across the animal kingdom including vertebrates, arthropods, mollusks, and annelids, but has been lost in many lineages such as nematodes, fruit fly, jawless fish, and tetrapods, concordant with a birth-and-death mode of evolution. All Gv proteins contain 5 G-box motifs characteristic of GTP-binding proteins and the expected acylation consensus sites in the N-terminal region. Sixty amino acid residues are conserved only among Gv, suggesting that they may constitute interaction sites for Gv-specific partner molecules. Overall Gv homology is high, on average 70% amino acid identity among vertebrate family members. The d(N)/d(S) analysis of teleost gnav genes reveals evolution under stringent negative selection. Genomic structure of vertebrate gnav genes is well conserved and different from those of the other 4 classes. The predicted full ORF of zebrafish gnav1 was confirmed by isolation from cDNA. RT-PCR analysis showed broad expression of gnav1 in adult zebrafish and in situ hybridization demonstrated a more restricted expression in larval tissues including the developing inner ear. The discovery of this fifth class of Galpha proteins changes our understanding of G protein evolution.

Evolution of the guanylate binding protein (GBP) genes: Emergence of GBP7 genes in primates and further acquisition of a unique GBP3 gene in simians.

Guanylate binding proteins (GBPs) are major players in the host immunity, providing defense against bacterial and viral invaders. Multigene families may suffer different processes of evolution. Gene families related to the immune system usually follow the birth-and-death evolution process, where duplicated genes can be deleted, gain new functions or become non-functional. We analyzed publicly available primate GBP sequences and their genomic organization and observed that GBP7 genes appear to have emerged from a duplication of GBP4 and seem to be only present in primates. Furthermore, GBP3 genes are only present in Simiiformes and probably originated from GBP1 genes. Finally, a duplication event occurred in the GBP6 in Tarsiiformes and became functional which might also explain the duplication of GBP6 in New World monkeys and Cercopithecidae. Taken together, this study provides new knowledge on the evolution of GBPs in primates and suggests that a revision of the GBPs nomenclature is necessary.

A distinct mechanism regulating a pollen-specific guanine nucleotide exchange factor for the small GTPase Rop in Arabidopsis thaliana.

Rop/Rac small GTPases are central to diverse developmental and cellular activities in plants, playing an especially important role in polar growth of pollen tubes. Although it is established that a class of plant-specific RopGEFs promotes the activity of Rop/Rac through the catalytic PRONE (Plant-specific Rop nucleotide exchanger) domain, not much is known about how RopGEF function is controlled to allow a spatiotemporally regulated Rop activity. To understand such a process in pollen, we performed functional analysis with a pollen-specific RopGEF, AtRopGEF12. Overexpression of AtRopGEF12 had minimal phenotypic effects, whereas overexpression of a C-terminally truncated version disturbed tube growth, suggesting that the C terminus was inhibitory to GEF function. In contrast to non-pollen-expressed RopGEFs, pollen-expressed RopGEFs have conserved C termini. A phospho-mimicking mutation at an invariant serine within the C terminus of AtRopGEF12 resulted in loss of the C-terminal inhibition, suggesting that phosphorylation regulates GEF activity in vivo. The PRONE domain of AtRopGEF12 (PRONE12) was not sufficient to induce isotropic tube growth. We used mbSUS to show that AtRopGEF12 interacts with an Arabidopsis pollen receptor kinase AtPRK2a through its C terminus, and BiFC to show that they interact in pollen tubes. Coexpression of AtRopGEF12 and AtPRK2a caused isotropic growth reminiscent of that seen upon overexpression of a constitutively active (CA) Rop. Coexpression of AtPRK2a with an N-terminally truncated AtRopGEF12 did not induce isotropic growth, indicating a positive role for the N-terminal domain. Our results suggest a mechanism by which the noncatalytic domains of pollen-specific/enriched RopGEFs regulate PRONE function, leading to polarized pollen tube growth.

IAN family critically regulates survival and development of T lymphocytes.

The IAN (immune-associated nucleotide-binding protein) family is a family of functionally uncharacterized GTP-binding proteins expressed in vertebrate immune cells and in plant cells during antibacterial responses. Here we show that all eight IAN family genes encoded in a single cluster of mouse genome are predominantly expressed in lymphocytes, and that the expression of IAN1, IAN4, and IAN5 is significantly elevated upon thymic selection of T lymphocytes. Gain-of-function experiments show that the premature overexpression of IAN1 kills immature thymocytes, whereas short hairpin RNA-mediated loss-of-function studies show that IAN4 supports positive selection. The knockdown of IAN5 perturbs the optimal generation of CD4/CD8 double-positive thymocytes and reduces the survival of mature T lymphocytes. We also show evidence suggesting that IAN4 and IAN5 are associated with anti-apoptotic proteins Bcl-2 and Bcl-xL, whereas IAN1 is associated with pro-apoptotic Bax. Thus, the IAN family is a novel family of T cell-receptor-responsive proteins that critically regulate thymic development and survival of T lymphocytes and that potentially exert regulatory functions through the association with Bcl-2 family proteins.

G protein subtype specificity of rhodopsin intermediates metarhodopsin Ib and metarhodopsin II.

Rhodopsin is one of the members of the G protein-coupled receptor family that can catalyze a GDP-GTP exchange reaction on the retinal G protein transducin (Gt) upon photon absorption. There are at least two intermediate states, meta-Ib and meta-II, which exhibit direct interaction with Gt. Meta-Ib binds to GDP-bound Gt, while meta-II forms a complex with Gt having no nucleotide, suggesting that meta-Ib is a state that initially interacts with Gt. Here we investigated whether or not meta-Ib exhibits specific interaction with G protein similar to meta-II, by examining the binding efficiencies of meta-Ib and meta-II to Gialpha and its mutants whose C-terminal 11 amino acids were replaced with those of Goalpha, Gqalpha and Gsalpha. The affinity of meta-Ib to the C-terminal 11 amino acids of Gtalpha was similar to those of Gialpha and its mutant with Goalpha's C-terminal 11 amino acids, whereas meta-II exhibited affinity to the C-terminal 11 amino acids of Gialpha mutant with Goalpha's C-terminal 11 amino acids about half of what was seen for Gtalpha and Gialpha. Both intermediates exhibited no affinity to the Gialpha mutants containing the C-terminal 11 amino acids of Gqalpha and Gsalpha. These results suggested that meta-Ib is the state that exhibits specific interaction with G protein as meta-II does, although meta-Ib exhibits a slightly lenient binding selectivity compared to that of meta-II.

Rho family GTPases: the cytoskeleton and beyond.

Until recently, members of the Rho family of GTPases were considered primarily to be regulators of the distinct structures making up the actin cytoskeleton. Several Rho GTPases have now also been shown to play an important role in cell transformation. In addition, Cdc42, Rac and Rho activate transcription, providing a possible mechanism for their role in growth control.

How Ras-related proteins talk to their effectors.

More and more effectors for the Ras-related protein superfamily are being discovered and it is emerging that these GTP-binding proteins interact with more than one effector to generate more than one cellular signal. Atomic details for the interaction of Rap/Ras with one of the effectors, the protein kinase c-Raf-1, have recently become available by X-ray structure analysis. The implications for the specificity of the signal transduction pathway, and how the GTP-dependent switch mechanism modulates the interaction with effectors will be discussed here, using Ras as a paradigm.

A region of the muscarinic-gated atrial K+ channel critical for activation by G protein beta gamma subunits.

Complementary DNAs encoding two types of inwardly rectifying K+ channels, GIRK1 and IRK1, have been cloned from rat atrium and mouse macrophage, respectively. GIRK1 expressed in Xenopus oocytes was activated by acetylcholine when m2 muscarinic acetylcholine receptor was coexpressed. The acetylcholine-induced activation of GIRK1 was enhanced by coexpression with the G protein beta 1 gamma 2 subunit but not the beta 1 gamma 1 or alpha subunits. Deletion of the C-terminus of GIRK1 impaired the channel activation associated with the beta 1 gamma 2 subunit. Moreover, replacement of the C-terminus of IRK1 with that of GIRK1 produced a chimera channel that was activated by the beta 1 gamma 2 subunit, whereas intact IRK1 was not activated by the beta 1 gamma 2 subunit. These findings define the C-terminus of GIRK1 as a regulatory region for the G protein beta gamma subunit.

Evolutionary substitution of two amino acids in chloroplast SRP54 of higher plants cause its inability to bind SRP RNA.

The chloroplast signal recognition particle (cpSRP) consists of a conserved 54 kDa subunit (cpSRP54) and a unique 43 kDa subunit (cpSRP43) but lacks SRP-RNA, an essential and universally conserved component of cytosolic SRPs. High sequence similarity exists between cpSRP54 and bacterial SRP54 except for a plant-specific C-terminal extension containing the cpSRP43-binding motif. We found that cpSRP54 of higher plants lacks the ability to bind SRP-RNA because of two amino acid substitutions within a region corresponding to the RNA binding domain of cytosolic SRP54, whereas the C-terminal extension does not affect RNA binding. Phylogenetic analysis revealed that these mutations occur in the cpSRP54 homologues of higher plants but not in most algae.

Structural stabilization of GTP-binding domains in circularly permuted GTPases: implications for RNA binding.

GTP hydrolysis by GTPases requires crucial residues embedded in a conserved G-domain as sequence motifs G1-G5. However, in some of the recently identified GTPases, the motif order is circularly permuted. All possible circular permutations were identified after artificially permuting the classical GTPases and subjecting them to profile Hidden Markov Model searches. This revealed G4-G5-G1-G2-G3 as the only possible circular permutation that can exist in nature. It was also possible to recognize a structural rationale for the absence of other permutations, which either destabilize the invariant GTPase fold or disrupt regions that provide critical residues for GTP binding and hydrolysis, such as Switch-I and Switch-II. The circular permutation relocates Switch-II to the C-terminus and leaves it unfastened, thus affecting GTP binding and hydrolysis. Stabilizing this region would require the presence of an additional domain following Switch-II. Circularly permuted GTPases (cpGTPases) conform to such a requirement and always possess an 'anchoring' C-terminal domain. There are four sub-families of cpGTPases, of which three possess an additional domain N-terminal to the G-domain. The biochemical function of these domains, based on available experimental reports and domain recognition analysis carried out here, are suggestive of RNA binding. The features that dictate RNA binding are unique to each subfamily. It is possible that RNA-binding modulates GTP binding or vice versa. In addition, phylogenetic analysis indicates a closer evolutionary relationship between cpGTPases and a set of universally conserved bacterial GTPases that bind the ribosome. It appears that cpGTPases are RNA-binding proteins possessing a means to relate GTP binding to RNA binding.

Phylogenetic and evolutionary analysis of the septin protein family in metazoan.

Septins, a conserved family of cytoskeletal GTP-binding proteins, were presented in diverse eukaryotes. Here, a comprehensive phylogenetic and evolutionary analysis for septin proteins in metazoan was carried out. First, we demonstrated that all septin proteins in metazoan could be clustered into four subgroups, and the representative homologue of every subgroup was presented in the non-vertebrate chordate Ciona intestinalis, indicating that the emergence of the four septin subgroups should have occurred prior to divergence of vertebrates and invertebrates, and the expansion of the septin gene number in vertebrates was mainly by the duplication of pre-existing genes rather than by the appearance of new septin subgroup. Second, the direct orthologues of most human septins existed in zebrafish, which suggested that human septin gene repertoire was mainly formed by as far as before the split between fishes and land vertebrates. Third, we found that the evolutionary rate within septin family in mammalian lineage varies significantly, human SEPT1, SEPT 10, SEPT 12, and SEPT 14 displayed a relative elevated evolutionary rate compared with other septin members. Our data will provide new insights for the further function study of this protein family.

The Mx GTPase family of interferon-induced antiviral proteins.

Mx proteins are interferon-induced members of the dynamin superfamily of large GTPases. They inhibit a wide range of viruses by blocking an early stage of the replication cycle. Studies in genetically defined mouse strains highlight their powerful action in early antiviral host defence.

Increase in the expression of a family of small guanosine triphosphate-binding proteins, rab proteins, during induced phagocyte differentiation.

Rab is a newly identified family of small G-proteins that share 35-70% homology with the yeast Sec4p and Ypt1p involved in the regulation of the secretory pathway. Mature phagocytes display functions requiring organized intracellular traffic and, for this reason, we questioned whether phagocyte differentiation could correlate with the increased expression of rab proteins. Rabbit antisera raised against the recombinant proteins rab1Ap, 2p, 4p, and 6p were able to detect the corresponding proteins in the human monoblast leukemic cell line U937. When these cells were induced to differentiate into monocyte/macrophage-like cells displaying functional characteristics of a normal phagocyte, rab1Ap, 2p, 4p, and 6p were increased and this correlated with an increase in the rab transcripts. Using a rab5 probe, we also observed an increased expression of the rab5 gene in differentiated cells. Similarly, differentiation of the human leukemic myeloblast HL60 cell line along either monocyte or granulocyte pathways induced an increased expression of the rab proteins. Rab proteins were also detected in human neutrophils and in guinea pig alveolar macrophages. As degranulation is one of the phagocyte functions acquired in the late stage of differentiation, we investigated whether rab proteins would be involved in this process. Although rab proteins were tightly membrane bound, none of them was detected in the specific or azurophil granules purified from human neutrophils. The increased expression of rab proteins in mature phagocytes suggests that they may promote functions highly developed in these cells.

The G proteins of the G alpha i and G alpha q family couple the bradykinin receptor to the release of endothelium-derived relaxing factor.

Bradykinin stimulates diverse functions in endothelial cells including the release of endothelium-derived relaxing factor (EDRF). Little is known, however, regarding the identity of the G protein(s) involved. Here we demonstrate that G proteins of the G alpha i and G alpha q family are coupled to the bradykinin receptor (BKR) in bovine aortic endothelial cells by using specific antisera directed against the COOH-terminal region of G alpha i2 (P4), G alpha i3 (EC), and G alpha q (QL). These antisera are specific since their effects are blocked by the decapeptides from which they were derived. The degree of receptor-G protein coupling was assessed by the formation of high affinity agonist binding sites (HABS) and GTP hydrolysis. In a concentration-dependent manner, the QL antisera reduced HABS and GTPase activity by 65 and 60%, respectively, and effectively abolished them in membranes from pertussis toxin-treated cells. The combination of P4 and EC antisera produced a loss of HABS (41%) and GTPase activity (40%) comparable to the effects of pertussis toxin. These findings indicate that G alpha i and G alpha q proteins mediate the cellular responses to bradykinin in bovine aortic endothelial cells and support the observation that bradykinin-stimulated EDRF release is relatively insensitive to pertussis toxin.

Polymorphisms of the chicken antiviral MX gene.

The Mx gene was originally found in laboratory mice in an infection experiment using influenza virus (Lindermann, 1962). Almost all of the mouse strains in that experiment died from the infection, and only the A2G strain had resistance to the virus. This resistant character was shown to be inherited as a single autosomal dominant trait (Lindermann et al., 1963; Lindermann, 1964; Haller et al., 1979). A congenic mouse strain was established by introducing the Mx+ allele of the A2G resistant strain into the Mx- sensitive inbred strain BALB/c (Staeheli et al., 1984). By immunizing parental BALB/c mice with extracts of interferon (IFN)-treated cultured cells from congenic BALB/c-Mx+ mice, a specific antibody against Mx protein was obtained (Horisberger et al., 1983; Staeheli et al., 1985). The Mx protein was detected in the nucleus of IFN-alpha/beta-treated mouse cells by immunofluorescence using the anti-Mx antibody (Dreiding et al., 1985). Thereafter, by using the antibody as an indicator, cDNA encoding the Mx protein was cloned from a cDNA library constructed from IFN-treated cells of congenic BALB/c-Mx+ mice (Staeheli et al., 1986a). IFN-treated Mx+ mouse cells contained a 3.5-kb Mx mRNA in the Northern blot, while Mx- cells failed to express the transcript. The functional Mx+ gene from an A2G mouse was found to contain 14 exons and encode 631 amino acids. The Mx- allelic mouse strains were found to be missing sequence of exons 9 through 11 or to contain a point mutation that converts lysine at position 389 to a stop codon (Staeheli et al., 1988). If these polymorphisms of the Mx gene could be detected in domestic animals, it would be possible to produce breeds that show resistance to infectious diseases.

Endothelin action on pituitary lactotrophs: one receptor, many GTP-binding proteins.

The endothelins are a family of hormones that have a biphasic action on pituitary lactotrophs. The initial effect is stimulatory, followed later by inhibition that persists long after the agonist has been removed. Recent research has uncovered several G protein pathways that mediate these effects.

GGAPs, a new family of bifunctional GTP-binding and GTPase-activating proteins.

G proteins are molecular switches that control a wide variety of physiological functions, including neurotransmission, transcriptional activation, cell migration, cell growth. and proliferation. The ability of GTPases to participate in signaling events is determined by the ratio of GTP-bound to GDP-bound forms in the cell. All known GTPases exist in an inactive (GDP-bound) and an active (GTP-bound) conformation, which are catalyzed by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs), respectively. In this study, we identified and characterized a new family of bifunctional GTP-binding and GTPase-activating proteins, named GGAP. GGAPs contain an N-terminal Ras homology domain, called the G domain, followed by a pleckstrin homology (PH) domain, a C-terminal GAP domain, and a tandem ankyrin (ANK) repeat domain. Expression analysis indicates that this new family of proteins has distinct cell localization, tissue distribution, and even message sizes. GTPase assays demonstrate that GGAPs have high GTPase activity through direct intramolecular interaction of the N-terminal G domain and the C-terminal GAP domain. In the absence of the GAP domain, the N-terminal G domain has very low activity, suggesting a new model of GGAP protein regulation via intramolecular interaction like the multidomain protein kinases. Overexpression of GGAPs leads to changes in cell morphology and activation of gene transcription.